The families of 16 children born with serious heart defects did not receive the compassion, empathy and support they needed from staff at Leeds teaching hospitals trust and in some cases felt pressured to have terminations, an NHS investigation has found.

Leeds, where children's heart surgery was temporarily suspended last year over fears that death rates were too high, was given a clean bill of health for its clinical performance.

But the damning report into paediatric cardiology at Leeds general infirmary outlining the experiences of 16 families who complained of poor care at the unit has prompted apologies from both NHS England and the Leeds teaching hospitals NHS trust, which runs the hospital.

Parents felt they were being pressured to have terminations when the heart defect was detected in pregnancy, and were left alone and in distress after the diagnosis.

After the births, some say they were not told that doctors believed the baby would die. One couple waited three years for an operation only to discover that their child was not on the waiting list. Of the children involved, six are known to have died.

The review of the families' complaints about Leeds was carried out by the independent case reviewer, Professor Pat Cantrill. The complaints related to care between 2009 and 2013.

The mother of a baby called Tom told Cantrill: "They did the scan and then I went into a room where there was a doctor and a nurse. I was told my baby had half a heart.

"There was no compassion. I cried. The doctor said that the recommendation was to have a termination. I asked if there were other options and I was told I could go to full term and have the baby and then it would die or have the baby and then have surgery but that was not recommended. I was given a booklet and two days to make a decision.

"I was told not to look things up on the internet. I was sent to the antenatal clinic and waited from 2 o'clock until 5 o'clock. I was exhausted. My father went and asked for someone to see me. The staff had not been told about me.

"Then a doctor rang me at home on the Friday for my decision. I said I did not want a termination. I was told it was the biggest mistake of my life."

The families were sometimes given leaflets to take home but felt they did not have enough information to make a decision. "Some were left waiting in a distressed state, or in rooms on their own, and in one case left in a corridor," the report said.

The mother of another baby, Aziz, was urged to think about termination. "They seemed against me continuing with the pregnancy. As a Muslim I believe that abortion is wrong. They did not seem to understand," she told Cantrill.

After the birth, some said there was no plan for the care of the child.

John, who was breathless, sweaty, blue and slept most of the time, "was on the 'wait-and-see/as-and-when-required' path. Alarm bells starting ringing when a consultant at our local hospital questioned why no care plan was in place when John was so poorly," said on of his parents.

Many were distressed by the lack of distraction when necessary tests were carried out. The mother of Sally said: "When they took blood it was awful. They would hold her down. They had 12 attempts to get blood by four different doctors. She was so distressed and so were we.

"At the other hospital it could not have been more different. They have a distraction room and they play videos whilst they are taking blood. She can cope with it now."

Some parents said they were not told that the heart could not be repaired and any treatment was only palliative – to relieve symptoms.

"We were waiting to receive a letter for Shona to go into hospital for her heart surgery. I was a nervous wreck," said a mother. "She started to deteriorate. I contacted the hospital. They made me feel as though it was me and that I was being over protective and that I would just have to wait.

I said that we needed to see someone and eventually we saw the cardiologist. The scan did not show anything different. We had waited for three years for her surgery but when we saw the doctor she told us that Shona was inoperable and that she was not on the waiting list."

One mother was called by the children's hospice without knowing the hospital had referred the child. Families told of delays to their children's treatment, which they believed made it less likely to be successful.

Some talked of a lack of support after their child had died. "After Tim died the shutters seemed to come down. There should be counselling provided for parents who have lost their child," said a parent.

Not all the experiences were bad, the families acknowledged, but some said care from the cardiology service that had been good had deteriorated over the years.

The stories she heard, said Cantrill, "were all heartfelt, moving and sincere. All the families were saddened to find themselves in a position where they had lost confidence in the care provided for their children and for them as a family. They want the services for children with congenital heart conditions both nationally and locally to learn from their experience. They want services for children and their families to improve."

She made a series of recommendations for the trust, other heart units and NHS England.

The trust apologised to the families and said it had already made changes, but the deputy director of NHS England, Mike Bewick, warned that lessons must be learned by all those involved in the care of such vulnerable children.

"Such experiences cannot be defended," he said.

Julian Hartley, chief executive, and Yvette Oade, chief medical officer at Leeds teaching hospitals trust said they were glad the children's heart unit had been found to be safe and running well. "We are very sorry however, that the 16 families who shared their stories with [the review] felt we did not provide the care they had a right to expect … we sincerely apologise to those families and will of course, ensure we learn from what they had to say and improve our services as a result of this."

The report was published by NHS England on the day that Sir Ian Kennedy – who chaired the inquiry into failures in babies' heart surgery at the Bristol royal infirmary over a decade ago – met families whose children with heart defects died at another hospital in the city, the Bristol Royal Hospital for Children. Kennedy is helping to set up an inquiry into their concerns, at the request of Sir Bruce Keogh, NHS England's medical director.

"I have to say that I feel a great sense of sadness that I find myself here in Bristol – 13 years after my initial report – hearing once again the anger and distress of parents," said Kennedy. "The families want a robust independent process. We have made good progress in finding the way forward and there is still more work to do. We hope to get things moving with some urgency."

Four inquests on children who have died following heart operations in Bristol have exposed failings in care, breakdowns in communication and, at times, an apparent lack of empathy with parents when they flagged up concerns about treatment.

The parents of two of the youngsters, Luke Jenkins, seven, and Sean Turner, four, who died in 2012 within a month of each other at the Bristol royal hospital for Children, have strongly expressed the belief that staff did not take their concerns seriously.

Faye Valentine, the mother of Luke, said she and her partner, Stephen, were made to feel as if they were a nuisance when they flagged up fears about their son's recovery.

"We weren't being listened to," she said. "They thought we were being over-anxious and asking too many questions. They ignored us. We weren't asking stuff for the fun of it. We had serious issues and they ignored us."

The parents of four-year-old Sean Turner, who like Luke was treated in ward 32, the children's cardiac ward, said there had found a "lack of leadership, accountability and communication" at the hospital.

The trust insists that it has made fundamental changes to the way both children and their parents are cared for on ward 32. Parents are now asked regularly if they have concerns – and any worries are noted and what actions taken to address them recorded. In addition parents can write their views into the official patient records. Next to every child's bed is information about how they can raise concerns formally.